Term
| What are the three major classes of RNA polymerase in Eukaryotic RNA synthesis? |
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Definition
RNA Polymerase I
RNA Polymerase II
RNA Polymerase III |
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Term
| What does RNA Pol I primarily do? |
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Definition
| Codes for all rRNA's except for 5s |
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Term
| What does RNA Pol II primarily do? |
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Definition
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Term
| What does RNA Pol III primarily do? |
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Definition
| Codes for all tRNA's and rRNA 5s |
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Term
| Why is mt Pol in Eukaryotes sensitive to Rifampin? |
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Definition
| mitochondrial DNA and RNA processes are very similar to bacterial processes. This is why Rifampin at high doses can have a toxic effect |
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Term
| Where does most rRNA synthesis occur? |
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Definition
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Term
| What is the purpose of pseudo-uradine and and 2' O methylation in the synthesis of rRNA? |
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Definition
| Both of these aid in the folding of rRNA into the 3D structure it has to assume to be useful |
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Term
| What is the code that is analagous to the pribnow box but for Eukaryotes? |
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Definition
| The TATA box. Not as universal as the pribnow box but many genes use the TATA box as a promoter. |
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Term
| What transcription factor binds to the TATA box? |
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Definition
| TBP (TATA binding protein), this is also a signal for the machinery to commence synthesis |
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Term
| What is the consensus sequence for the TATA box? |
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Definition
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Term
| Typically RNA transcription starts on what base pair? |
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Definition
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Term
| Once transcription is initiated, how is the initiation machinery disassembled so that transcription can continue? |
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Definition
| The protein machinery is disassembled by phosphorylation of the CTD (c terminal domain) by TFIIH |
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Term
| Does mRNA synthesis require Helicase? |
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Definition
| Yes, the double strand still needs to be unwound if it is to be transcribed |
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Term
| In the synthesis of inducible or regulated genes (genes used less commonly) does the machinery change at all? |
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Definition
| Yes, the machinery becomes much more complex including activation factors, histone-modifying enzymes and chromatin-remodeling complexes |
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Term
| Where do the proteins of elongation reside? |
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Definition
| On the CTD of RNA polymerase II |
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Term
| What are the important proteins of elongation that reside on the CTD tail of RNA polymerase? |
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Definition
Splicing and Capping proteins.
Splicing Proteins cut out introns from the precursor mRNA
Capping Proteins put a cap on the 5' end of the mRNA |
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Term
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Definition
| 7-methylguanosine does a 5'->5' connection on the end of the RNA |
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Term
| What is the function of Capping? |
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Definition
| The function is two-fold. 1) capping prevents RNAse from degrading the RNA and 2) Capping is an integral cog in the recognition of mRNA by Ribosomes |
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Term
| How does capping help the translational machinery work? |
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Definition
| The 5' cap of an mRNA recruits eIF's (Eukaryotic Initiation Factors) to form a complex that can be recognized and used by Ribosomes |
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Term
| What is the biochemical process of splicing (unassisted by spliceosome)? |
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Definition
2 hydroxyl attacks
First a 2' hydroxyl attack on 5' end of RNA makes a unique 2'->5' phosphodiester bond
-this forms the lariat structure
second hydroxyl attack reconnects the RNA and cleaves off the lariat structure |
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Term
| What happens to the lariat after the intron is excise? |
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Definition
| Most degrade but some are used for coding purposes |
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Term
| Why can RNA molecules behave much like enzymes (have catalytic function)? |
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Definition
| The unique ability of the 2'->5' nucleophillic attack mechanism illustrated in the lariat formation gives RNA catalytic function. This differs fundamentally from DNA |
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Term
| What are the three critical sequences necessary for intron splicing? |
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Definition
5' end: GU
3' end: AG
and an A in the middle to form the lariat |
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Term
| What are the key components of the spliceosome? |
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Definition
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Term
| What does the spliceosome do? |
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Definition
| It assists in the splicing of Eukaryotic mRNA. Note this is not always necessary as some splicing occurs without the spliceosome |
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Term
| U4 and U1 are created by what RNA polymerase? |
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Definition
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Term
| U6 is coded for by which polymerase? |
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Definition
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Term
| What is alternative splicing? |
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Definition
| This is also called exon shuffling. This occurs during splicing where some exons are deactivated yielding a whole new protein. |
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Term
| What is the stop sequence for termination of mRNA synthesis? |
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Definition
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Term
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Definition
| Cleveage and Poly A Specificity Factor. Recognizes sequence and brings along CstF |
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Term
| What is CstF and what is it's function? |
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Definition
| Cleavage stimulating Factor. Stimulates cleavage of the newly formed mRNA |
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Term
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Definition
| Poly A adds a variable length A tail to the 3' end of newly synthesized RNA |
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Term
| What is the function of the Poly A tail? |
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Definition
| The Poly A tail has two functions. 1) It is a measure of the lifespan of a mRNA (the longer it is, the longer the mRNA survives and codes for proteins), 2) it is used as recognition by the translation machinery |
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Term
| What is post-transcriptional editing? |
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Definition
| This is changes made to mRNA after transcription |
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Term
| What is a good example of post-transcriptional editing? |
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Definition
Apolipoproteins:
These mRNA's are modified dependent on where they are resulting in different proteins
Shortened in intenstine to make a protein that works with Chylomicrons |
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Term
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Definition
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Term
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Definition
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Term
| What is the UTR of a mRNA? |
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Definition
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